Importing quant.sf file to tximport

Question

[yvarg009]

Hi! I am new to R studio and using tximport. I have a quant.sf file that I need to import to R studio using tximport, however I am stuck. This is what I have gotten so far. I have downloaded the tximport as suggested by this website.

Link: https://bioconductor.org/packages/3.12/bioc/html/tximport.html

Link: https://bioconductor.org/packages/release/data/experiment/html/tximportData.html

I have been following this guide;https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html but to no avail.

This is what I have so far;

What should the next step be?

I would highly appreciate the help or any suggestions! THANK YOU! (:

I tried doing various ways and I would end up getting errors. Unfortunately, I did not take screenshots earlier, I kept it opened thinking it wouldn't erase on me or remove me from what I did but I guess that was not the case.

[yvarg009]

Should I follow the guide as it is given? or is there a different suggestion? Are there any tutorials available that I am able to see that would explain this?

This is what I have so far;

https://ibb.co/fq7ZdYL

https://ibb.co/rHHxc49

Answer 1

[rpolicastro]

All of your errors are because you don't have the hg19 transcript database installed. Most of those packages are on bioconductor, so go to their bioconductor page and follow the installation instructions.

For example the command to install the hg19 transcript database is

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")

If you get a prompt asking whether packages should be updated at the end of installation, enter either a or n into the terminal if you want to update all, or skip updates.

[yvarg009]

Thank you! Okay, I installed the packages from bioconductor. How do I import the quant.sf file ?

[rpolicastro]

The tximport function from the tximport library can import that file.

[yvarg009]

Would I write it, for example;

txi.tx <- tximport(files, type

I don't know what would come after that. I have my quant.sf file saved to my desktop. Is there any specific place I should have the file saved to?

[rpolicastro]

From the screenshot it looks like you're on a Mac, so the file is probably ~/Desktop/quant.sf, and the type is probably "salmon".

[yvarg009]

Thank you so much!

https://ibb.co/mBhf41L

This is what I get. I installed txtimport

[rpolicastro]

You need to load the library with library("tximport") or explicitly state the namespace of the function with tximport::tximport(). Also, your argumenst to the function need to be characters (strings), so surround each one with quotes.

[yvarg009]

https://ibb.co/sRStdS0

This is what I have so far, with the recommendations you gave me.

[rpolicastro]

You need to put quotes around the file path.